Professional Medical & Scientific Blog of Autumn Kulaga

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Just Learning

Sometimes it is hard to be motivated ( in general fear and money are pretty good ones). Even when curiosity and/or creativity exists, there is sometimes a gap between thinking and execution. However (usually) once you conjure up a little drive the gap closes and you pick up momentum. Luckily I got back into the swing of things during the first week.

This summer my main time consumers are going to be a:

Multimedia class

Flash Animation

Advance Imaging techniques

Mimics, DICCOM data from Osirix database, Kidney, Aorta

& Pathophysiology.

Over the next 7 weeks I will also get an introduction to the surgical field, clinical sciences and the opportunity to present my research proposal (August 1st).

Stay tuned as I will explain the above images/ projects in future posts. And yes… there will be some flash.

Earlier in the semester I introduced my final project for Computer Visualization (Origination). I decided to create an environment to display the bacteria Giardia Intestinalis. This is a pretty intense little critter. I learned about this guy while taking Medical Microbiology at Towson University. It is amazing how many microscopic creatures surround us constantly!

After I came up with my idea, I needed to roughly figure out what I wanted my scene to look like. I created the following sketch as a general composition and color scheme. I didn’t want to make the sketch too detailed, as I was sure bits of the image would changed as I started modeling and texturing in 3DS max.

Once I had the sketch I proceeded to create the scene. One of the goals of this assignment was to demonstrate an understanding of render passes. Render passes, generated in a 3d modeling program when you render your scene, allow output of different channels. This allows for post-processing, or editing, in Photoshop. One of the benefits of this technique is ease of post render modifications (i.e. – its a big time saver). My gallery provides most of the passes I rendered out such as alpha, lighting, specular, ambient, diffuse and zdepth .

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Then after hours of modeling, texturing, lighting, rendering AND Photoshop editing I was able to create this master piece:

As a tip to compositing newbies, don’t hesitate to generate a channel using matte. I didn’t do this when I rendered my ‘main Giardia’ render pass, so the environment in this render pass had all parts rendered, including parts unseen in the beauty pass. I was able to paint this out in the alpha channels, but had the shape been more complex I would have re-rendered with a matte layer. Another tip, try placing your zDepth as an alpha channel in Photoshop. Then blur the image using lens blur filter ( once in the filter options, you have to select the channel from a drop down menu). This magical trick keeps from having to use depth of field in the camera settings and saves time rendering. I also really liked working with the lighting channel. I can’t really explain how, but it does nice things.

As always there are edits I would like to make, but like any good artwork I learned a lot during this process. The overall color scheme changed however I am okay with that. The image needed to look darker and feel more unpleasant. In this sense the lighting worked out, and overall I think it came out better then I originally sketched. I hope you enjoy!

The molecular world is a fascinating place. What captivates me is the visuals we accept as a part of the molecular environment tend to be theoretical. This environment is outside of a human’s visual capacity, therefore in order to better understand the form of the chemical compounds we come up with visual mechanisms to understand their structures (of course we use math and very expensive equipment to verify our theories). After establishing a foundation in chemistry, human understanding of chemical properties led to the capability of visualizing complex chemical structures. A few of the visual mechanisms developed are backbone, ribbon, ball & stick, space-filled and surface models. Through apprehension of structural form, a chemical compound’s functional mechanisms can be better understood.

This passed Wednesday our class learned how to extract and manipulate files from the Protein Data Bank and use them to visualize chemical models. We explored different methods and programs such as Chimera and mMaya. Another program we did not go over, but worth exploring, is BioBlender.

The model I have decided to play with is the human growth hormone (GH). This hormone is manufactured in the anterior pituitary gland, then released into the blood stream where it then travels to the liver. In the liver GH stimulates the production of insulin-like growth factor 1 (IGF-1). IGF-1 then leads to the growth of long bones as well as facilitate growth of muscle cells.

After extracting the data from the Protein Data Bank website, I slightly modified the surface model in Chimera. I played around with the colors of the different chemicals, and tried to understand how each molecule was broken down. Sometimes the protein can be divided into different chains.

Link to WebGL - Human GH Surface Model

Link to WebGL - Human GH Ribbon Model

My next step is to use take the extracted PDB file and display the molecule in a 3D environment. Stay tuned for sweet visualizations ahead!

When someone asks, “What is medical illustration?”, the answer is not very straight forward ( and sometimes those of us within the field can even be surprised as to how “all encompassing” the term can be). The first thing that usually pops into others minds is Frank H. Netter. Don’t get me wrong, he was good at what he did. However there are many more, very talented artists which practiced before him and helped establish the field.

One of histories profound medical illustrators is Max Brodel. Brodel was from Germany and came to America in his late 20’s to work for Howard Kelly. In 1911 he helped establish, and began to teach at, the first school of medical illustration, Art as Applied to Medicine at Johns Hopkins School of Medicine.

Brodel is also well known for an illustration technique he developed, carbon dusting. Carbon dusting, as I have come to understand it, is a gradual process of adding carbon dust and applying it with a carbon pencil to a specific type of board. My class’s assignment was to recreate a carbon dust illustration by Brodel, not with carbon dust, but using Adobe Photoshop. The image I chose is shown above, a transverse section of the brain I started by doing the drawing, scanning it and in photoshop applying a mid-tone grey to the whole drawing. Next, I worked through gradually shading parts, starting large and working into small details. To do this I used a combination of shape adjusting brush with zero hardness and varying shades of gray. Sometimes I made the brush mode ‘multiply’. At other times, when needing to darken whole areas, I used the burn tool. Then I went back to lighten, add highlights, to necessary parts of the illustration. For this I used a white brush, never the dodge tool.

This was one of those pieces you could work on FOREVER, so I mainly focused on the bottom portion of the brain. The process was very enjoyable. It was easy to get lost in the details, but nice when I zoomed out and could see the piece coming together as a whole.

I have been thinking a lot lately about making an interactive by creating imagery in Adobe Illustrator and exporting it to a HTML 5 canvas tag. Then using JavaScript to add functionality. And I finally had some time to download and try out the Plug-ins! Check it out!

It may look like ‘just an image’ but it is not. If you right-click ‘inspect element’ you will see it is a canvas tag. If you look in the head tag you will see the javascript used to draw the element on the page. 😀 I pretty excited. Nothing moves yet so it is pretty boring, but this is the beginning to wonderful interactive anatomical adventures! Once I figure out how each layer and each object is labeled, it should be pretty straight forward to add functionality.

One is provided by adobe, but the one I just used is by visitmix.com. When you scale the page ( ‘Command’/’Ctrl’ + ‘+’) the image does not scale with it. The Adobe Plug in is supposed to export images that scale.

I will keep you updated as I get more time to implement the other plug in, and as I get to add some functionality. But in the mean time feel free to check out the plug-ins:

You can have as many objects as you want in a scene, but until you have light you will not see anything. Everything will cease to have form until there is light. I put together a few images that help show RGB lighting and 3 point lighting technique.

RGB Lighting

Most think it is objects which gives form to an environment, when really it is the addition of light. I think this is missed because 3D modeling applications automatically add a default light to the scene. To start thinking about light, our class assemble three cameras, one green, one blue, and one red, all pointing to one spot equidistant from each other. The result is shown above. This was a neat exercise. It allowed me to clearly understand blending of light.

3Point Lighting

Also I wanted to share learning about Three Point Lighting. Three point lighting (here is a tutorial) is a generic technique also used in many instances such as 3D modeling, photography, and even figure drawing sessions. It is called 3 point lighting because the technique uses three lights, a key light, a fill light and a rim light. This exercise helps one think about where lights are placed to give proper definition and form to a scene.

This first image is not 3point lighting system but a basis of comparison because it uses a skylight. Notice how the skylight evenly lights the scene and provides no shadows.

After removing the skylight, we then added the first of the three lights, the key light. A key lights purpose is to be the main light source. This lights is to be placed above the camera and to the left ( ~45-60 degrees). An upper left light source provides the most aesthetically pleasing ( i.e. “accepted” ) source of light.

Next was a fill light. The purpose of the fill light is pretty much in the name, to help “fill” the scene with more light. This light was placed on the opposite side of the camera ( about the same distance as the key light ( ~45-60 degrees), however it can be placed above, below or parallel to the camera. With the fill light try to introduce little to no shadow.

The last light was the rim light, which is placed opposite the camera and behind the subject matter. This light helps to introduce some light to dark areas in the image. Even in the shadows you still want a little light, just to show subtle details.

The renders I provided are a little blown out by the addition of the third light. I encourage following the tutorial in order to learn for yourself. You don’t even need a 3D modeling program, just some objects and three lamps!